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Title: IDENTIFICATION AND ANNOTATION OF 11,363 CLONES FROM A MURINE DOPAMINE NEURON-SPECIFIC CDNA LIBRARY USING SEQUENCING AND VARIOUS BIOINFORMATICS APPROACHES

Author
item LI, MING
item ZHANG, D
item TAYLOR, WILLIAM
item Donovan, David
item BECKER, KEVIN

Submitted to: Society for Neuroscience Abstracts and Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 6/2/2004
Publication Date: 6/2/2004
Citation: Li, M.D., Zhang, D., Taylor, W., Donovan, D.M., Becker, K.G. 2004. Identification and annotation of 11,363 clones from a murine dopamine neuron-specific cdna library using sequencing and various bioinformatics approaches. [abstract]. Society for Neuroscience Abstracts and Proceedings. 809.10.

Interpretive Summary:

Technical Abstract: Brain dopamine (DA) neurons play a key role in movement and cognition and mediate the reinforcing effects of drugs of abuse. Such neurons also have been implicated in several neuropsychiatric illnesses, including Parkinson's disease, schizophrenia, and drug addiction. Although it is well accepted that DA neurons play a significant role in brain function, their molecular characteristics remain largely unknown. To gain a better understanding of the genes expressed in DA neurons, we sequenced 11,363 cDNA clones selected randomly from a murine DA neuron-specific cDNA library and annotated them using various of bioinformatics approaches. On the basis of this sequence information, we identified 10,268 clones whose sequence qualities were considered reliable and subjected them to further bioinformatics analysis. Pair-wise comparisons revealed that the 10,268 clones represent 4,793 non-redundant clones. To determine if these non-redundant clones represent known genes, hypothetical ones, or novel hypothetical ones, we searched the NCBI GenBank, LocusLink, and RefSeq, and UCSC Mouse Genome databases using USSC Blat and the NCBI Blast and MapView programs. This search yielded 1,536 LocusLink genes, which represent 563 unique genes. Furthermore, we predicted 1,840 novel genes that are not present in the NCBI LocusLink database. However, when these novel genes were subjected to pair-wise comparisons for redundancy checking, we found that they represent 334 novel hypothetical genes. Additionally, we still have 1,317 non-redundant clones that showed no 'hit' with genome sequences available in the public databases. In summary, our sequence and bioinformatics analyses revealed at least 900 genes that are expressed in mouse DA neurons, which should represent a valuable resource for determining how expression profiles change under different neuropsychiatric conditions